...is a soft ionization method used for the detection of quasimolecular ions, hence one can calculate a molecular formula. Another useful approach is to study gas phase reactions or apply CI for structure elucidation purposes. See some interesting books. A CrossRef search on Chemical Ionization Mass spectrometry [Long] [Short].

One general problem with CI is the generally lower intensity of peaks observed compared to EI. Another problem is that no large spectral library exist (as the NIST DB for EI spectra) which makes identification a very unpleasant experience. But with tuning one can generate mixed spectra which contain EI and CI data, that can be (somehow) search in EI libraries. Only few labs use chemical ionization which was very popular in 1980s but there is a growing trend in CI because of sensitivity for certain chemicals in negative mode and of course the molecular ion detection.

There are several neat tricks which show the importance of chemical ionization for gas chromatography based structure elucidation. We outlined them in several talks using our Seven Golden Rules concept. As the detection of the molecular ion is the general enabler for all following interpretations and predictions (including substructures, retention indices) soft ionization techniques are of extremely importance. See my COSMOS slides [PDF].

Since large molecule databases are available (KEGG, PubChem, ChemSpider) it is also possible to download such molecules and perform molecular calculations which could help the chemical ionization structure elucidation process. One example is the prediction of proton affinities. One could for instance calculate what kine of molecular ion for certain substance classes can be expected (in case of CH4 as reaction gas a [M-H]+ will be observed in positive CI ionization for alkanes). Other approaches would be the prediction of other observed adducts.

So every metabolomics lab which is not only performing GC-MS based metabolite profiling, but is also is interested in discovery processes, should have at least one accurate mass, accurate isotopic abundance, fast scanning (10-20 spectra per second or better) chemical ionization mass spectrometer available.